[Chimera-users] electron density map

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 28 09:31:14 PDT 2016


Hi Liuqing Chen!

The step value is whether the map is being viewed at full detail (step 1 = every point in the map) or being subsampled (step 2, every other point, step 3, every third point, etc.).

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#threshcolor>

The map values shown in the histogram where you control the level are simply the values taken from the input map file.  They are not processed by Chimera.  If you mean how it decides what level to show first, that is described here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf>

Sorry, I don’t know if Coot handles the values the same way or differently from Chimera.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Apr 28, 2016, at 3:26 AM, 陈柳青 <519198561 at 163.com> wrote:
> 
> Hi!
> I display the 2Fo-Fc map in chimera, but i wonder what the meaning of step 1, step2,etc in volume viewer. 
> The other question is what the relationship between the level in chimera volume viewer and Coot map level ?
> Best regards
> --
> Liuqing Chen




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